10/07/08

Journal Club

Simone Sanna-Cherchi

OUTLINE

Basis of Admixture Mapping as strategy do identify disease-associated genes

Papers

Implications of MYH9 association to FSGS and non-diabetic ESRD in African Americans

LINKAGE DISEQUILIBIRUM

• The probability of 2 independent events co-occurring is the product of the individual probabilities

• LD is defined as the non-random association of alleles at different loci on the same chromosome/haplotype

Genotype at Marker A allows prediction of genotype at marker B

Marker A Marker B

Allele 1 Allele 1

LINKAGE DISEQUILIBIRUM

WHAT CAUSES LD

• Mutation

• Admixture

• Selection

• Random genetic drift

WHAT CAUSES LD

• Mutation

• Admixture

• Selection

• Random genetic drift

DECAY OF LD WITH TIME

AVERAGE EXTENT OF LD

Half-life of LD: Distance at which average D’ drops below 0.5:

– US: 60kb; Nigerians: 5kb (Reich et al.)

– Sardinia, Finns, US, UK: ~50kb (Eaves et al.)

– British ancestry: ~50kb (Abecasis et al.)

– Sardinian subisolate: 1-4 Mb (Zavattari et al.)

GENE MAPPING VIA GWAS:IMPLICATIONS

At least 300,000 markers for GWAS in Caucasians (1 SNP every 10kb)

At least 1 million markers for GWAS in Africans (1 SNP every 3kb)

Statistical issues: multiple test adjustments require large data sets to identify variants with small effect

Limitations to less common diseases in which sample sizes are in the order of hundreds of patients (ex FSGS)

ADMIXTURE MAPPING HYPOTHESIS

• Disease allele has different frequencies in source populations

• For cases, disease allele site will be enriched for one ancestry

African Americans: Admixture

~80%

~20% MS

ProstateCancer

ADMIXTURE MAPPING: MALD

Chromosomal admixture segments

Smith, Nat Rev Genet 2005

EXPERIMENTALLY distinguish African and European ancestry

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European American Frequency

We

st

Afr

ica

n F

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ue

nc

y

The most informative ~1% of SNPs provide powerful information about ancestry

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0% 20% 40% 60% 80% 100%

European American Frequency

We

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Afr

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Advantages:

-Cases only

-Less than 2000 SNPs for GWAS

POWER OF MALD ANALYSIS

Patterson, Am J Hum Genet 2004

MAPPING BY SEGMENT ANCESTRY

Patterson, Am J Hum Genet 2004

LINKAGE DISEQUILIBRIUM RESOLUTION

DISEASES SUITABLE FOR

MALD

HYPOTHESES AND STUDY DESIGN

Cumulative lifetime risk for ESRD is 2.1% in European Americans (EA) and 7.5% in African Americans (AA)

AA have higher risk for several forms of nephropathy: diabetic, hypertensive, lupus nephritis, FSGS (4-fold risk) and HIVAN (18- to 50- fold risk)

MALD: 1,272 SNPs across the genome in 190 AA FSGS and 222 matched controls

Fine Mapping and identification of MYH9

Extension of association to MYH9 in 241 AA FSGS and 611 controls

Replication in 125 EA FSGS and 221 controls

Extension to 525 AA ESRD (241 hypertensive, 284 diabetic) and 192 controls

SUBJECTS

MALD RESULTS

MYH9 FINE MAPPING

20 MYH9 SNPs:

- Pronounced difference in allelic differences btw African Yorubans and Europeans

- Possible functional significance

- Strong LD with previously typed SNPs associated to FSGS even after correction for local ancestry

12 SNPs in 4 neighboring genes as control

GENOTYPIC ASSOCIATION SUGGESTS A RECESSIVE MODEL

ASSOCIATION WITH IDIOPATHIC FSGS, HIVAN AND ESRD

HAPLOTYPE ASSOCIATION

CONCLUSIONS

MALD is a increasingly efficient method to discover genes for complex traits in admixed populations

MALD require less genotyping (200-500 times less markers compared to GWAS), thus reducing costs and, most importantly, increasing power (less correction for multiple testing) and simplifying computation

Amenable for traits with pronounced differences in risk in the parental populations and for which large sample sizes are difficult to recruit

Most of the difference in risk of developing FSGS in African Americans compared to European Americans is due to variants in MYH9

Variants at MYH9 account for the higher risk of non-diabetic ESRD in African Americans, especially ESRD due to hypertensive nephrosclerosis

1,354 SNPs for MALD

All ESRD 1,372 cases / 806 controls

DM 703 cases / 806 controls

Non-DM 669 cases / 806 controls

HTN 347 cases / 806 controls

FSGS 87 cases / 806 controls

GN 126 cases / 806 controls

HIV 69 cases / 806 controls

Grey=DM ESRD

Black=non-DM ESRD

Grey= controls

Black= non-DM ESRD

MALD RESULTS

MYH9: nonmuscle myosin heavy chain, class II, isoform A

110 kb, 41 exons, highly conserved among mammals and very similar to other nonmuscle myosin isoforms

Abundantly expressed in kidney, liver, platelets

Involved in different cellular functions, including cell polarity, architecture and trafficking

Rare mutations in MYH9 cause several autosomal dominant conditions, such as May-Hegglin anomaly, Fechtner, Epstein and Sebastian syndromes, featuring macrothrombocytopenia with variable association of sensorineural deafness, cataract, neutrophil Dohle-like bodies and glomerular disease (Alport-like)

MYH9 KO mice show embryonic lethality, while heterozygous are normal except low penetrance hearing loss

MYH9: nonmuscle myosin heavy chain, class II, isoform A

In the kidney is expressed in the glomerulus (podocytes), peritubular capillaries and tubules

It takes part of the actin cytoskeleton, regulating contractility and cell integrity

One patients carrying a MYH9 mutation in whom kidney biopsy was performed at early kidney involvement showed focal podocyte foot process effacement and loss of slit diaphragm at the EM

Since Mendelian forms of FSGS are caused by mutations in genes encoding for proteins of the actin cytoskeleton (ACTN4, CD2AP and others) it is tempting to speculate that more common variants in MYH9 can predispose to podocyte damage and FSGS and HTN

ADMIXTURE MAPPING MARKERS

• Theoretically:– Much less markers sufficient

• Practically:1. Develop marker set for admixture mapping:

Look for high frequency differencesor

2. Use many markers, ignore non-informative